Data & ReproBioinformatics & GenomicsFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-metagenomics-metaphlan

Maintainer FreedomIntelligence · Last updated April 1, 2026

Marker gene-based taxonomic profiling using MetaPhlAn 4. Provides accurate species-level relative abundances using clade-specific markers. Use when accurate taxonomic profiling is needed and computational resources are limited, or for comparison with HMP/other MetaPhlAn studies.

OpenClawNanoClawAnalysisReproductionbio-metagenomics-metaphlan🧬 bioinformatics (gptomics bio-* suite)bioinformatics — metagenomics & microbiomemarker

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-metagenomics-metaphlan

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

CLI: metaphlan sample.fastq --input_type fastq -o profile.txt.
Profile the species composition of my metagenome" → Determine species-level relative abundances from shotgun metagenomic reads using clade-specific marker gene alignment. CLI: metaphlan sample.fastq --input_type fastq -o profile.txt.
MetaPhlAn 4 uses ~5M clade-specific markers from 26,970 species-level genome bins. Supports both short reads (bowtie2) and long reads (minimap2).
metaphlan sample.fastq.gz \ --input_type fastq \ --output_file profile.txt.

Source Doc

Excerpt From SKILL.md

MetaPhlAn processes PE as single file or concatenated

metaphlan reads_R1.fastq.gz,reads_R2.fastq.gz
--input_type fastq
--output_file profile.txt
--mapout sample.map.bz2


## First run - save intermediate mapping

metaphlan sample.fastq.gz \
    --input_type fastq \
    --mapout sample.map.bz2 \
    --output_file profile.txt

## Rerun with different settings without realigning

metaphlan sample.map.bz2 \
    --input_type mapout \
    --output_file profile_v2.txt